BINF630:IntroductiontoBioinformatics IosifVaismanEmail:ivaisman@gmu.edu Whatis GlobalDNS IP DomainNameSystem 250 2,032,268 21,862,63372,398,092DatafromISC(January2000) TLD Top-leveldomainDomainsHosts Client-ServerModel CLIENT PROTOCOL SERVER Client-ServerModel WEBBROWSER HTTP WEBSERVER TELNETCLIENT FTPCLIENT TCP/IPFTP UNIXHOST FTPSERVER MAILCLIENT IMAP/POP MAILSERVER NEWSREADER NNTP NEWSSERVER UniformResourceLocator(URL) protocol://host.domain[:port]/path/filename ftp-ananonymousFTPserver(ftp://ftp.pdb.pdb.gov)-asession(://nun.oit.unc.edu) Networkapplicationsinscience •VirtualLaboratory•VirtualLibrary•VirtualConference•VirtualClassroom Networkcollaboration Real-timedatasharing--exchangeofinformationbetweenremoteparticipantsintheprojectResourcessharing--remoteesstotheinstrumentsputersResourcesintegration--simultaneoususeofremoteinstrumentsputers Bioinformaticsservers Remotedataess--databsesearch,cross-linksbetweenthedatabases puting--useofserver’sprocessingcapabilities(sequencealignment,structureprediction,homologymodeling) Infospacenavigation--pointerstotheavailableresources Bioinformaticsservers Real-timeAsynchronous Digitalinformationcycle CreationandcaptureStorageandmanagementRightsmanagementSearchandessDistribution Electronicpublishing Quality(peerreview,retrospectiveevaluation)Reliability(stabilityofserves,controloveralterations,properarchivingandmirroring) HypertextFunctionalityinScientificLiterature ActivereferencesForwardingreferencesDynamicpublishing Ethical,Legal,andEconomicalIssuesofElectronicPublishing IntellectualpropertyrightsOwnershipofinformationInformationasmodity DatabasesinBioinformatics MolecularDatabases Nucleicacidsequences:GenBank,DNADataBankofJapan,EMBLNucleotideSequenceDatabase Nucleicacidstructures:NDB-NucleicAcidDatabase Proteinsequences:PIR-ProteinInformationResource,SWISS-PROT Proteinstructures:PDB-ProteinDataBank,NRL_3D Physicalproperties:BiologicalMacromoleculeCrystallizationDatabase,BioMagResBank Molecularimages:SWISS-3DIMAGE,MoleculesRUS MolecularDatabases NCBIintegratedsearchandretrievalsystem Entrez NCBIDatabases •nr-Allnon-redundantGenBankCDStranslations+PDB+SwissProt+PIR •month-AllneworrevisedGenBankCDSreleasedinthelast30days •swissprot-thelastmajorreleaseoftheSWISS- PROT proteinsequencedatabase(no updates) •yeast-Yeast(haromycescerevisiae)proteinsequences. •E.coli-E.coligenomicCDStranslations •pdb-Sequencesderivedfromthe3-dimensionalstructureBrookhavenProteinDataBank •kabat-Kabat'sdatabaseofsequencesof immunological interest Database Database databasefile recordfieldcharacter acollectionofrelatedstructuredinformationaboutentitiesacollectionofrecords asetoffieldsasinglecharacteristicofanentity asymbolusedindatafield ExampleofaGenbankentry LOCUSDEFINITION ACCESSIONNIDKEYWORDSSOURCE ORGANISM REFERENCEAUTHORS TITLE JOURNALMEDLINEREFERENCEAUTHORSTITLE JOURNALMEDLINE VIBHALUXA3141bpDNA BCT 15-FEB-1996 V.harveyiluciferasealphaandbetasubunit(luxAandluxB)genes, completecds. M10961M13494 g155174 luciferase. VibrioharveyiDNA. Vibrioharveyi Eubacteria;Proteobacteria;gammasubdivision;Vibrionaceae; Vibrio. 1(bases1to1838) Cohn,
D.H.,Mileham,
A.J.,Simon,
M.I.,Nealson,
K.H.,Rausch,
S.K., Bonam,D.andBaldwin,
T.O. NucleotidesequenceoftheluxAgeneofVibrioharveyiandthe completeaminoacidsequenceofthealphasubunitofbacterial luciferase
J.Biol.Chem.260(10),6139-6146(1985) 85207595 2(bases1745to3141) Johnston,
T.C.,Thompson,
R.B.andBaldwin,
T.O. NucleotidesequenceoftheluxBgeneofVibrioharveyiandthe completeaminoacidsequenceofthebetasubunitofbacterial luciferase
J.Biol.Chem.261(11),4805-4811(1986) 86168191 ExampleofaGenbankentry FEATURES Location/Qualifiers gene 707..1774 /gene="luxA" CDS 707..1774 /gene="luxA" /codon_start=
1 /product="luciferase
alphasubunit" /db_xref="PID:g155175" /transl_table=11 /translation="MKFGNFLLTYQPPELSQTEVMKRLVNLGKASEGCGFDTVWLLEH HFTEFGLLGNPYVAAAHLLGATETLNVGTAAIVLPTAHPVRQAEDVNLLDQMSKGRFR FGICRGLYDKDFRVFGTDMDNSRALMDCWYDLMKEGFNEGYIAADNEHIKFPKIQLNP SAYTQGGAPVYVVAESASTTEWAAERGLPMILSWIINTHEKKAQLDLYNEVATEHGYD VTKIDHCLSYITSVDHDSNRAKDICRNFLGHWYDSYVNATKIFDDSDQTKGYDFNKGQ WRDFVLKGHKDTNRRIDYSYEINPVGTPEECIAIIQQDIDATGIDNICCGFEANGSEE EIIASMKLFQSDVMPYLKEKQ" BASE
COUNT 883a665c741g852t ORIGIN 1bpupstreamofEcoRIsite. 1atgacgacgggcaaaaatagtttgtgcactgtttatcactg 61aagggcacacaaaacattggcttgattgcggcaagtctctcagctcgtgttatgaa 121gttatctctgatctggagctgtcttttctgattactgcggttggtgtggtgaacttgcgt 181gacacactagaaaaagcgcttggttttgattcagtttatcgaa ....